Figure Size in R Markdown

Rmarkdown: Explicitly specify the figure size of a plot within a chunk

So I haven't found an alternative to subchunkify(), however I did solve the issue with it reusing the same plots on each loop iteration (though I haven't dug into why it was yet).

I added an id argument to subchunkify() and included it in the file name, and then within my loop/map I created an id value that would be a combination of variables within each iteration that would be unique for each one.

subchunkify <- function(g, fig_height=7, fig_width=5, id = NULL) {
  g_deparsed <- paste0(deparse(
    function() {g}
  ), collapse = '')

  sub_chunk <- paste0("
  `","``{r sub_chunk_", id, "_", floor(runif(1) * 10000), ", fig.height=", fig_height, ", fig.width=", fig_width, ", echo=FALSE}",
  "\n(", 
    g_deparsed
    , ")()",
  "\n`","``
  ")

  cat(knitr::knit(text = knitr::knit_expand(text = sub_chunk), quiet = TRUE))
}

So I'm not sure why the runif in subchunkify was failing to result in distinct file names on each iteration. My suspicion is that it has something to do with how knitr caching works. I noticed that if a subsequent iteration of my loop ended up going through the same conditional chain to produce graph A, then graph A would be reused everywhere that the condition chain matched. However if an iteration went off on a different conditional branch to produce graph B, it would correctly generate a new graph. (However then graph B would be reused in all places with the same conditional branch ending).

This still doesn't explain why me introducing a unique file name with id works, but using runif doesn't since in both cases the file name should be unique, so this is only a guess.

So I guess if anyone else is having problems, I have a solution here but not an explanation. Very unsatisfying but does the trick!

Changing figure size (Rstudio, Rmarkdown, Shiny)

This is how I use Shiny in Rmarkdown. This is a answer I used. You can adjust your shiny shinyApp() function with the options argument.

WITHOUT FIX(notice scroll bar)

With the code below

---
title: "Shiny in Rmarkdown"
output: html_document
runtime: shiny
---

```{r echo = FALSE, warning=FALSE, message=FALSE }
library(tidyverse)
library(shiny)

server <- function(input, output, session) {
    
    trends <- reactive({
        req(input$sel_year)
        mpg %>%
            filter(year %in% input$sel_year)
        
    })
    
    output$plot <- renderPlot({
        ggplot(
            data = trends(),
            mapping = aes(x = trans)
        ) + 
            geom_bar()
    })
}

ui <- fluidPage(
    selectInput(
        inputId = "sel_year",
        label = "Choose Year",
        list("1999", "2008")
    ),
    plotOutput("plot")
)

shinyApp(ui = ui, server = server, options = list(height = 750))
```

Size of plot in R-Markdown

You can change the pot size in an R-Markdown code chunk by setting the fig.height= and fig.width= chunk arguments:

```{r fig.height=8, fig.width=8}
ggplot(iris) + 
  geom_line(aes(x = Sepal.Length, y = Sepal.Width), size = 0.5)
```

Adjust for large figure size in Shiny RMarkdown report

I never followed up with the answer I figured out... here's an approach that doesn't require adding a slider for anyone else facing the same problem in the future, (1) using my example and (2) using a more minimal version with built-in datasets:

Version 1

---
title: "Test"
author: "R User"
date: "9/7/2021"
output: html_document
runtime: shiny
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(ggplot2)
library(dplyr)
# example data
df <- data.frame(
  subject = c(rep("A", 1000), rep("B", 1000), rep("C", 1000)),
  course = rep(paste0("Course ", as.character(1:300)), 10),
  value = rnorm(3000)
)
```

## Modify figure size

I would like to modify the figure size so the ridgelines are still readable when grouped by course, either by making the figure size larger overall or allowing the user to scroll down the figure.

```{r, echo=FALSE}
inputPanel(
  selectInput("group", label = "Group",
              choices = c("subject", "course"))
)

plot_height <- reactive({
  df %>%
    pull(get(input$group)) %>%
    unique() %>%
    length()
})

renderPlot({
  ggplot(df, aes(y = !!as.symbol(input$group), x = value)) +
    geom_boxplot() +
    theme_minimal()
}, height = function() { 50 * plot_height() })
```

Version 2

---
title: "Dynamic Plot Height"
author: "Natalie O'Shea"
date: '2022-05-31'
output: html_document
runtime: shiny
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(dplyr)
library(ggplot2)
```

```{r}
inputPanel(
  selectInput("grouping", label = "Select grouping:", 
              choices = c("supp", "dose"))
)

plot_height <- reactive({
  ToothGrowth %>%
    pull(get(input$grouping)) %>%
    unique() %>%
    length()
})

renderPlot({
  ToothGrowth %>%
    ggplot(aes(y = len)) +
    geom_histogram() +
    facet_wrap(~get(input$grouping), ncol = 1)
}, height = function() { 100 * plot_height() })
```

RMarkdown/Knitr, matching physical figure size and displayed HTML size

When you say out.height="5.29in", out.width="5.89in", those values are written into the HTML output as height and width attributes of the img. But height and width are expressed in pixels, so you'll end up with a figure about 5 pixels square.

I don't use Powerpoint, but is there a way to specify the image size in pixels, e.g. "589px" or something similar? Then it will use the same scale as the browser, and things should be consistent.

---

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